From 38d634541e55ce0b17d079b50452de4445dd9256 Mon Sep 17 00:00:00 2001
From: rogoersTPH <roland.goers@swisstph.ch>
Date: Tue, 23 Aug 2022 16:35:14 +0200
Subject: [PATCH] Add vaccMinPrevDoses and vaccMaxCumDoses to
 deploy_cont_compat

---
 R/xml_interventions_deploy.R                  | 34 ++++++++++++---
 man/deploy_cont_compat.Rd                     | 12 ++++++
 .../testthat/test-xml_interventions_deploy.R  | 43 +++++++++++++++++++
 3 files changed, 84 insertions(+), 5 deletions(-)

diff --git a/R/xml_interventions_deploy.R b/R/xml_interventions_deploy.R
index b1099e1..d5a6cdc 100644
--- a/R/xml_interventions_deploy.R
+++ b/R/xml_interventions_deploy.R
@@ -457,6 +457,14 @@ deploy_it_compat <- function(baseList, component = "ITN", cumulative = FALSE,
 ##' @param varyCov Default is FALSE , for varying coverage
 ##' @param targetAgeYrs Age at which intervention is received (1=1 year) e,g.
 ##'   c(0.25,0.33 ,0.75)
+##' @param vaccMinPrevDoses Applies to vaccines only: vaccine doses are only
+##'   deployed by this deployment if the previous number of doses (for the
+##'   component deployed) is at least this number. Needs to be of the same
+##'   length as targetAgeYrs.
+##' @param vaccMaxCumDoses Applies to vaccines only: vaccine doses are only
+##'   deployed by this deployment if the previous number of doses (for the
+##'   component deployed) is less than this number. Needs to be of the same
+##'   length as targetAgeYrs.
 ##' @param coverage Coverage, either fixed (integer) or as a variable
 ##'   ("@@IPTcov@@"), same order as for target age years
 ##' @param restrictToSubPop f this element is specified, deployment is
@@ -464,6 +472,7 @@ deploy_it_compat <- function(baseList, component = "ITN", cumulative = FALSE,
 ##' @export
 deploy_cont_compat <- function(baseList, component = "IPTi", begin = "2019-01-01",
                                end = "2030-01-01", targetAgeYrs = NULL,
+                               vaccMinPrevDoses = NULL, vaccMaxCumDoses = NULL,
                                coverage = NULL, varyCov = FALSE,
                                restrictToSubPop = NULL) {
   ## Generate output list
@@ -510,14 +519,29 @@ deploy_cont_compat <- function(baseList, component = "IPTi", begin = "2019-01-01
   }
 
   when <- as.data.frame(cbind(targetAgeYrs, coverage))
+  if (!is.null(vaccMinPrevDoses)) {
+    when["vaccMinPrevDoses"] <- vaccMinPrevDoses
+  }
+  if (!is.null(vaccMaxCumDoses)) {
+    when["vaccMaxCumDoses"] <- vaccMaxCumDoses
+  }
+
   temp <- list()
   for (i in seq_len(nrow(when))) {
     temp <- list(
-      deploy = list(
-        coverage = when[i, "coverage"],
-        targetAgeYrs = when[i, "targetAgeYrs"],
-        begin = begin,
-        end = end
+      deploy = c(
+        list(coverage = when[i, "coverage"]),
+        if (!is.null(vaccMinPrevDoses)) {
+          list(vaccMinPrevDoses = when[i, "vaccMinPrevDoses"])
+        },
+        if (!is.null(vaccMaxCumDoses)) {
+          list(vaccMaxCumDoses = when[i, "vaccMaxCumDoses"])
+        },
+        list(
+          targetAgeYrs = when[i, "targetAgeYrs"],
+          begin = begin,
+          end = end
+        )
       )
     )
 
diff --git a/man/deploy_cont_compat.Rd b/man/deploy_cont_compat.Rd
index 0c54a1c..4e38050 100644
--- a/man/deploy_cont_compat.Rd
+++ b/man/deploy_cont_compat.Rd
@@ -10,6 +10,8 @@ deploy_cont_compat(
   begin = "2019-01-01",
   end = "2030-01-01",
   targetAgeYrs = NULL,
+  vaccMinPrevDoses = NULL,
+  vaccMaxCumDoses = NULL,
   coverage = NULL,
   varyCov = FALSE,
   restrictToSubPop = NULL
@@ -27,6 +29,16 @@ deploy_cont_compat(
 \item{targetAgeYrs}{Age at which intervention is received (1=1 year) e,g.
 c(0.25,0.33 ,0.75)}
 
+\item{vaccMinPrevDoses}{Applies to vaccines only: vaccine doses are only
+deployed by this deployment if the previous number of doses (for the
+component deployed) is at least this number. Needs to be of the same
+length as targetAgeYrs.}
+
+\item{vaccMaxCumDoses}{Applies to vaccines only: vaccine doses are only
+deployed by this deployment if the previous number of doses (for the
+component deployed) is less than this number. Needs to be of the same
+length as targetAgeYrs.}
+
 \item{coverage}{Coverage, either fixed (integer) or as a variable
 ("@IPTcov@"), same order as for target age years}
 
diff --git a/tests/testthat/test-xml_interventions_deploy.R b/tests/testthat/test-xml_interventions_deploy.R
index a5483ca..b8fda8d 100644
--- a/tests/testthat/test-xml_interventions_deploy.R
+++ b/tests/testthat/test-xml_interventions_deploy.R
@@ -355,4 +355,47 @@ test_that("deploy_cont_compat works", {
   )
 
   expect_equal(actual, expected)
+
+  ## vaccMinPrevDoses and vaccMaxCumDoses used
+  expected <- list(
+    interventions = list(
+      name = "All interventions",
+      human = list(
+        deployment = list(
+          name = "IPTi",
+          component = list(
+            id = "IPTi"
+          ),
+          continuous = list(
+            deploy = list(
+              coverage = 0.8,
+              vaccMinPrevDoses = 0,
+              vaccMaxCumDoses = 1,
+              targetAgeYrs = 0.8,
+              begin = "2019-01-01",
+              end = "2030-01-01"
+            ),
+            deploy = list(
+              coverage = 0.7,
+              vaccMinPrevDoses = 1,
+              vaccMaxCumDoses = 2,
+              targetAgeYrs = 0.16,
+              begin = "2019-01-01",
+              end = "2030-01-01"
+            )
+          )
+        )
+      )
+    )
+  )
+
+  actual <- deploy_cont_compat(
+    testlist,
+    targetAgeYrs = c(0.8, 0.16),
+    coverage = c(0.8, 0.7),
+    vaccMinPrevDoses = c(0, 1),
+    vaccMaxCumDoses = c(1, 2)
+  )
+
+  expect_equal(actual, expected)
 })